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DTAST: A Novel Radical Framework for de Novo Transcriptome Assembly Based on Suffix Trees

  • Jin Zhao
  • Haodi Feng
  • Daming Zhu
  • Chi Zhang
  • Ying Xu
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10954)

Abstract

In this article, we develop a novel radical framework for de novo transcriptome assembly based on suffix trees, called DTAST. DTAST extends contigs by reads that have the longest overlaps with the contigs’ terminuses. These reads can be found in linear time of the length of the reads through a well-designed suffix tree structure. Besides, DTAST proposes two strategies to extract transcript-representing paths: a depth-first enumeration strategy and a hybrid strategy based on length and coverage. Experimental results showed that DTAST performs more competitive than the other compared state-of-the-art de novo assemblers. The software with choice for either strategy is available at https://github.com/Jane110111107/DTAST.

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Jin Zhao
    • 1
  • Haodi Feng
    • 1
  • Daming Zhu
    • 1
  • Chi Zhang
    • 2
  • Ying Xu
    • 3
  1. 1.School of Computer Science and TechnologyShandong UniversityJinanChina
  2. 2.Department of Medical and Molecular GeneticsIndiana UniversityIndianapolisUSA
  3. 3.Department of Biochemistry and Molecular BiologyUniversity of GeorgiaAthensUSA

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